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Reposted by Mikaël Salson

Rayan Chikhi @rayanchikhi.bsky.social · Sep 3

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

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Mikaël Salson @mikael-salson.univ-lille.fr · Sep 5

They defended yesterday but, unfortunately, not as a duo!

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Mikaël Salson @mikael-salson.univ-lille.fr · Sep 4

A wonderful day for @bonsaiseqbioinfo.bsky.social, with @camillemrcht.bsky.social's and @npmalfoy.bsky.social's HDR defenses.
Congrats for the amazing work!

It's a great chance for the team to have you both!

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Mikaël Salson @mikael-salson.univ-lille.fr · Jul 21

Oh, she's undoubtedly going to talk about @peercommunityin.bsky.social, right?

Screenshot of an extract of a program in a bioinformatics conference.

Invited Presentation: Choosing journals for submission in popular topics
Confirmed Presenter: Laura ******, Elsevier

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 21

And one from @imartayan.bsky.social and @curiouscoding.nl at SEA in Venice on simd computation of minimizers

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 21

Two talks for Bonsai this Thursday, one from @mikael-salson.univ-lille.fr during ISMB presenting a compressed representation for viral MSAs,

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Mikaël Salson @mikael-salson.univ-lille.fr · Jul 21

There is no such thing as "AI peer review". AI is not a peer.

www.nature.com/articles/d41...

Scientists hide messages in papers to game AI peer review

Some studies containing instructions in white text or small font — visible only to machines — will be withdrawn from preprint servers.

www.nature.com

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 8

All Bonsai related communications during #JOBIM2025. Come meet us 👇🏻

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 9

Bonsai delegation enjoying #JOBIM2025 🌴and Bordeaux's weather

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Kristoffer Sahlin @ksahlin.bsky.social · Jul 2

I worked with Thomas during a three months research visit during his PhD, and it resulted in a paper in NAR. I highly recommend him. doi.org/10.1093/nar/...

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 3

Bonsai goes camping by the shore ☀️

Members enter the sea as the sun goes down

A picture of the group with pretty dusk colors and the beach in the background

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jun 18

On day 3 our PhD students Mathilde Girard, @bdegardins.bsky.social and Yohan Hernandez Courbevoie will present in the sequence algorithms session

JOBIM 2025 @jobim2025.bsky.social · Jun 16

⌚ Les inscriptions pour #JOBIM2025 se sont clôturées ce week-end. Merci pour votre participation, et rendez-vous à Bordeaux du 8 au 11 juillet ! 🌞

Mais avant ça, et si vous jetiez un œil au programme des communications orales ? 👀
Il est disponible sur notre site Internet ➡️ jobim2025.labri.fr

Journées Ouvertes en Biologie, Informatique et Mathématiques - 2025

jobim2025.labri.fr

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Ragnar {Groot Koerkamp} @curiouscoding.nl · Jun 19

It's hard to overstate how excited I am about suffixient sets and the new path decomposition variant!

This preprint is a quick writeup to go with Nicola's CPM talk yesterday.

I hope to eventually write a blog about it, but here's some conceptual highlights. 1/

arxiv cs.DS @arxiv-cs-ds.bsky.social · Jun 18

Ruben Becker, Davide Cenzato, Travis Gagie, Sung-Hwan Kim, Ragnar Groot Koerkamp, Giovanni Manzini, Nicola Prezza
Compressing Suffix Trees by Path Decompositions
https://arxiv.org/abs/2506.14734

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Camille Marchet ⚡ @camillemrcht.bsky.social · May 16

😊😊😊 Just grateful because some weeks are very good weeks for the team, and it's been one of them ☺️☺️☺️

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Mar 28

Bonsai group members will present 3 talks at @recombseq.bsky.social 2025 in Seoul recomb-seq.github.io/program/ excited to meet you there!

Program

RECOMB-seq is the RECOMB Satellite Conference on Biological Sequence Analysis

recomb-seq.github.io

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Camille Marchet ⚡ @camillemrcht.bsky.social · Mar 28

Fully funded positions + included travels between Simon Puglisi's and our group. Dm/email if you have questions.

Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Mar 28

Job offers: 1 funded PhD position and 1 postdoc in computational genomics between Univ Lille and Helsinki Uni, details: kamimrcht.github.io/webpage/jobs.html we're looking for candidates, please share 🙏🏻

PhD and Postdoc in computational genomics

CRIStAL, CNRS, Université de Lille

kamimrcht.github.io

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Mikaël Salson @mikael-salson.univ-lille.fr · Mar 13

Un mauvais clic plus tard, je confirme qu'on peut modifier après validation ! Ouf.

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Mikaël Salson @mikael-salson.univ-lille.fr · Mar 12

En appuyant sur le-dit bouton, j'ai toujours un doute !

« Vous êtes sur le point de valider et d'envoyer votre dossier de candidature pour l'offre n°XXXXX. En appuyant sur le bouton « Valider », vous confirmez votre accord final pour soumettre tous les documents et informations. »

"Accord final"🤔

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Mikaël Salson @mikael-salson.univ-lille.fr · Mar 12

Super, merci beaucoup !

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Mikaël Salson @mikael-salson.univ-lille.fr · Mar 12

Disons que le seul bouton s'appelle « Valider la candidature » et qu'il n'est activé qu'une fois que tous les champs et toutes les pièces ont été chargées. Ça me refroidit un peu de valider un dossier non finalisé… (mais j'envisage de tester sur un poste random).

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Feb 10

An example of k-mers data structures in action in a result result: with colleagues from CRCT Toulouse and IRMB Montpellier, we have identified an aberrant splicing mechanism in blood stem cells and certain aggressive forms of acute myeloid leukemia. 1/2

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Feb 10

Preprint alert! Can we enumerate how many k-mers lexicographic minimizers have? Yes! (implicitly). Looking forward to applications of this 👌🏻 work by Florian Ingels, @mikael-salson.univ-lille.fr @camillemrcht.bsky.social arxiv.org/abs/2412.17492

On the number of $k$-mers admitting a given lexicographical minimizer

The minimizer of a word of size $k$ (a $k$-mer) is defined as its smallest substring of size $m$ (with $m\leq k$), according to some ordering on $m$-mers. minimizers have been used in bioinformatics -...

arxiv.org

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recombseq.bsky.social @recombseq.bsky.social · Jan 23

🚨 Deadline Extended: Call for Papers - RECOMB-seq 2025 🚨

Great news! You now have an extra week to submit your work. 🎉

Updated Deadlines:
🔹 Abstract Registration: Jan 31, 2025
🔹 Submission: Feb 7, 2025

recomb-seq.github.io/papers/

Call for Papers

RECOMB-seq is the RECOMB Satellite Conference on Biological Sequence Analysis

recomb-seq.github.io

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Mikaël Salson @mikael-salson.univ-lille.fr · Dec 17

So ashamed I missed it!

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Lucile Veissier @lucileveissier.bsky.social · Dec 12

Présente à la convention des labos du CNRS, la seconde après celle de 2019

Antoine Petit annonce un nouveau label pour concentrer les efforts dans 25% des unités : les keylabs

La liste des labos est en finalisation, on vous en reparle bientôt dans @themeta.news

#VeilleESR

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